When Roy attacks Jim in the office, it isn't his first time hurting someone. Pam acts odd during her apology to Jim, and for the first time since the merger, he can't bring himself to ignore it. A two or three part AU based around “Cocktails” (S3,E18) and “The Negotiation” (S3, E19).

This is such a bad summary, I promise the story is better!

Jim and Pam are CIA agents assigned to break a Scranton element of a smuggling ring. "Stamford" is a cover for Jim being recalled to Langley after confessing his feelings for Pam, but now he's coming back. And he has to recruit Dwight as an asset.

NOW COMPLETE. Set in AU S3. Spoilers through S3.

AU: Dunder Mifflin and the characters are real, but subject to a media and internet blackout about their own show. Pam gets suspicious when a simple search for "jam" returns an error code saying it is related to the show. 

 Set somewhere vaguely in an AU S2. 

It is Valentine's Day and Michael is throwing a party. Pam Goes to the party to blow off some steam and have fun. Pam gets a little drunk and gets the guts to do something she has been wanting to say for a long time.

It’s not as if she’s never seen his desk without him sitting there, because of course she has. He’s stayed home sick, made occasional—if unexciting—use of his vacation days, gone on sales calls — she knows what the office looks like when the shape of him is missing, when she glances up and there’s an absence where the slope of his shoulders is supposed to be.

As she settles in that first day of his absence, hangs her coat and takes her seat, Pam lets herself miss him as a coworker and as a best friend and that’s it. Work will be work, with or without Jim Halpert.

But that’s a lie, because of course it is.

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A series of one-shots retelling season 3 from Pam's perspective